The long term objective of this project is to construct a detailed restriction map of overlapping lambda clones using an existing coarse NotI restriction map of the cyanobacterium, Agmenellum quadruplicatum PCC 7002. This map will allow us to understand how the Agmenellum genome controls photosynthesis. Tbe contig mapping experiments takes advantage of a technique used to group lambda clones from a overlapping clone library into ensembles of clones. Each ensemble belongs to a unique large pulsed field restriction fragment. Tbe advantages to grouping clones into ensembles are: a) a limited number of clones are needed to construct a contig, b) contig assembly proceeds along the physical restriction map of an organism, c) and ensembles of clones derived from large overlapping pulsed field restriction fragments can be used to create physical restriction maps. Once the detailed physical map is constructed, a genetic map can be made using hybridization probes of existing cyanobacterial clones. The organization of photosynthetic genes in relationship to other important genes of biochemical pathways such as nitrogen metabolism (glnA), amino acid biosynthesis, carbohydrate synthesis (Calvin cycl), protein synthesis (rrnA, rrnB, rps genes) and RNA and DNA metabolism (rpo genes, recA, and AquI methylase) will be compared using genomic transcript mapping. Light controls the growth and replication of this bacterium, in darkness it will down regulate photosynthetic pathways by diminishing transcripts of these genes. Upon illumination these gene transcripts become overly abundant reaching levels several fold greater than exists in steady state fight. The differential response of transcripts to light will be mapped on the genome by screening a separated and ordered clone library from labelled transcripts isolated in the dark and in the Eght. The techniques used here in should be applicable to map many prokaryotic genomes including those of pathogenic organisms whose detailed genomic organization or expression of certain genes are involved in a toxigenic or pathogenic phenotype.